Diversity of soil bacteria and fungi communities in artificial forests of the sandy-hilly region of Northwest China

Soil erosion is a serious issue in the sandy-hilly region of Shanxi Province,Northwest China.There has been gradual improvement due to vegetation restoration,but soil microbial community characteristics in different vegetation plantation types have not been widely investigated.To address this,we analyzed soil bacterial and fungal community structures,diversity,and microbial and soil environmental factors in Caragana korshinskii Kom.,Populus tomentosa Carr.,Populus simonii Carr.,Salix matsudana Koidz,and Pinus tabulaeformis Carr.forests.There were no significant differences in the dominant bacterial community compositions among the five forest types.The alpha diversity of the bacteria and fungi communities showed that ACE(abundance-based coverage estimator),Chao1,and Shannon indices in C.korshinskii forest were significantly higher than those in the other four forest types(P<0.05).Soil organic matter,total nitrogen,and urease had a greater impact on bacterial community composition,while total nitrogen,β-glucosidase,and urease had a greater impact on fungal community composition.The relative abundance of beneficial and pathogenic microorganisms was similar across all forest types.Based on microbial community composition,diversity,and soil fertility,we ranked the plantations from most to least suitable as follows:C.korshinskii,S.matsudana,P.tabulaeformis,P.tomentosa,and P.simonii.

Soil microbial community diversity and distribution characteristics under three vegetation types in the Qilian Mountains, China

Qilian Mountains in Northwest China is a significant ecological security barrier due to its distinctive geographic setting,which has significant biological resource and gene pool.In order to assess the soil quality and ecosystem health in this area,we identified the structural characteristics and functional groups of soil microbial communities.This study focused on Amidongsuo,a typical watershed of the Qilian Mountains,and researched the vertical distribution and dominant populations of soil microorganisms in different habitats,and the relationship between soil microorganisms and environmental factors.Soil microorganisms from three grassland plots,five shrubland plots,and five forest plots in Amidongsuo were studied using high-throughput sequencing.The Venn diagram showed that the types of bacteria were fewer than those of fungi in Amidongsuo.Soil bacteria Acidobacteriota,Proteobacteria,and Methylomirabilota as well as fungi Basidiomycota,Ascomycota,and Mortierellomycota played dominant roles in Amidongsuo,according to the LEfSe(linear discriminant analysis(LDA)effect size)and community structure analyses.According to the ANOSIM(analysis of similarities)result,for both bacteria and fungi,R values of grassland and shrubland were small(R^(2)=0.045 and R^(2)=0.256,respectively),indicating little difference between these two ecosystems.RDA(redundancy analysis)showed a closer relationship between soil nutrients and fungi,and a gradually decreasing correlation between soil nutrients and microorganisms with increasing soil depth.Bacteria were mainly affected by pH,nitrogen(N),and potassium(K),while fungi were mainly affected by K.Overall,fungi had more effect on soil quality than bacteria.Therefore,adjustment of soil K content might improve the soil environment of Amidongsuo in the Qilian Mountains.

Habitat influences on diversity of bacteria found on German cockroach in Beijing

Cockroaches are worldwide indoor pests carrying microorganisms of medical importance. German cockroaches （Blattella germanica） were sampled in five habitats （hospital, restaurant, office home, and market） in Beijing, and the bacteria were isolated from their external surface and alimentary tract and identified using a Biolog identification system. Cockroach densities significantly differed among habitats （market 〉 home 〉 office 〉 restaurant 〉 hospital）. However, no significant differences in bacterial abundance carried by individual German cockroaches （of either sex） were found among habitats. The bacterial abundance in the gut was significantly higher than that on the surface. There were no significant differences in bacterial species richness observed among habitats, sex, carrying position or their interaction. Cluster analysis showed that cockroach densities and bacterial abundance found in the market differed significantly from the other four habitats. The bacterial diversity was not significantly reduced in sensitive facilities such as hospital and restaurant, even though pesticide and bactericide were more frequently applied there. The implications of these findings were discussed in this article.

Diversity of bacterial lactase genes in intestinal contents of mice with antibiotics-induced diarrhea

AIM To investigate the diversity of bacterial lactase genes in the intestinal contents of mice with antibiotics-induced diarrhea.METHODS Following 2 d of adaptive feeding, 12 specific pathogenfree Kunming mice were randomly divided into the control group and model group. The mouse model of antibiotics-induced diarrhea was established by gastric perfusion with mixed antibiotics(23.33 m L·kg^(-1)·d^(-1)) composed of gentamicin sulfate and cephradine capsules administered for 5 days, and the control group was treated with an equal amount of sterile water. Contents of the jejunum and ileum were then collected and metagenomic DNA was extracted, after which analysis of bacterial lactase genes using operational taxonomic units(OTUs) was carried outafter amplification and sequencing.RESULTS OTUs were 871 and 963 in the model group and control group, respectively, and 690 of these were identical. There were significant differences in Chao1 and ACE indices between the two groups(P < 0.05). Principal component analysis, principal coordination analysis and nonmetric multidimensional scaling analyses showed that OTUs distribution in the control group was relatively intensive, and differences among individuals were small, while in the model group, they were widely dispersed and more diversified. Bacterial lactase genes from the intestinal contents of the control group were related to Proteobacteria, Actinobacteria, Firmicutes and unclassified bacteria. Of these, Proteobacteria was the most abundant phylum. In contrast, the bacterial population was less diverse and abundant in the model group, as the abundance of Bradyrhizobium sp. BTAi1, Agrobacterium sp. H13-3, Acidovorax sp. KKS102, Azoarcus sp. KH32 C and Aeromonas caviae was lower than that in the control group. In addition, of the known species, the control group and model group had their own unique genera, respectively.CONCLUSION Antibiotics reduce the diversity of bacterial lactase genes in the intestinal contents, decrease the abundance of lactase gene, change the lactase gene strains, and transform their structures.

Microbial diversity of soil bacteria in agricultural field contaminated with heavy metals

In this study we evaluated the bacterial diversity in a soil sample from a site next to a chemical industrial factory previously contaminated with heavy metals. Analysis of 16S rDNA sequences amplified from DNA directly extracted from the soil revealed 17 different bacterial types （genera and/or species）. They included Polyangium spp., Sphingomonas spp., Variovorax spp., Hafina spp., Clostridia, Acidobacteria, the enterics and some uncultured strains. Microbes able to tolerate high concentrations of cadmium （500μmol/L and above） were also isolated from the soil. These isolates included strains of Acinetobacter （strain CD06）, Enterobacter sp. （strains CD01, CD03, CD04 and CD08） （similar strains also identified in culture-independent approach） and a strain of Stenotrophomonas sp. The results indicated that the species identified from direct analysis of 16S rDNA of the soil can be quite different from those strains obtained from enrichment cultures and the microbial activities for heavy metal resistance might be more appropriately addressed by the actual isolates.

Family-level diversity of extracellular proteases of sedimentary bacteria from the South China Sea

Protease-producing bacteria and their extracellular proteases are key players in degrading organic nitrogen to drive marine nitrogen cycling and yet knowledge on both of them is still very limited. This study screened protease-producing bacteria from the South China Sea sediments and analyzed the diversity of their extracellular proteases at the family level through N-terminal amino acid sequencing. Results of the 16 S rRNA gene sequence analysis showed that all screened protease-producing bacteria belonged to the class Gammaproteobacteria and most of them were affiliated with different genera within the orders Alteromonadales and Vibrionales. The Nterminal amino acid sequence analysis for fourteen extracellular proteases from fourteen screened bacterial strains revealed that all these proteases belonged to the M4 family of metalloproteases or the S8 family of serine proteases. This study presents new details on taxa of marine sedimentary protease-producing bacteria and types of their extracellular proteases, which will help to comprehensively understand the process and mechanism of the microbial enzymatic degradation of marine sedimentary organic nitrogen.

Bacterial diversity in the sediments collected from the Shikoku Basin

Diversity of bacteria was studied in deep-sea sediments from the Shikoku Basin in the Northwest Pacific Ocean by PCR, RFLP and sequence analysis of 16S rDNA and comparing with Genbank database. Based on the RFLP profile generated, 77 clones from the 16S rDNA library were divided into 27 types. Phylogenetic analysis showed that the 27 independent clones fell into four groups: Proteobac-teria (62.96%), Chloroflexi (14.81%), Planctomycetes (14.81%) and Acidobacteria (7.41%). Among all sequenced clones, 6 were related to the sulfur or sulfate metabolism bacteria and the results also demonstrated that some bacteria in deep-sea sediments had relation to matter-energy circulation.

The diversity and potential function of endophytic bacteria isolated from Kobreasia capillifolia at alpine grasslands on the Tibetan Plateau, China

A total of 50 endophytic bacterial isolates were obtained from Kobreasia capillifolia at alpine grasslands in the Eastern Qilian Mountains on the Tibetan Plateau in China. Based on the sequencing and phylogenetic analysis of 16 S r DNA genes, all isolates phylogenetically related closely to Bacillus, Acinetobacter, Stenotrophomonas, Brevundimonas, Arthrobacter, Curtobacterium, Paenibacillus, Plantibacter, Promicromonospora, Serratia, and Microbacterium, among which Bacillus was the predominant genus（47.8% of the total number of endophytic isolates）. These isolates possessed different biological functions. In 50 endophytic bacteria, 42 isolates produced indole acetic acid（IAA） on King medium. There were seven isolates showing potency of mineral phosphate solubilization in Pikovaskaia＇s（PKO） liquid medium. Seven isolates exhibited antagonistic effect against Fusarium avenaceum, Colletotrichum coccodes and Phoma foveata. This was the first report on diversity and plant growth promotion of endophytic bacteria from K. capillifolia on alpine grassland in the Eastern Qilian Mountains, Chain. It is essential for revealing the relationship among plant, microorganism, and the special environment because the potential function of endophytic bacteria made a contribution to the interactions of plants and endophytic bacteria.

Bacterial Community Structure and Diversity in a Black Soil as Affected by Long-Term Fertilization

Black soil(Mollisol) is one of the main soil types in northeastern China. Biolog and polymerase chain reactiondenaturing gradient gel electrophoresis(PCR-DGGE) methods were used to examine the infiuence of various fertilizer combinations on the structure and function of the bacterial community in a black soil collected from Harbin,Heilongjiang Province. Biolog results showed that substrate richness and catabolic diversity of the soil bacterial community were the greatest in the chemical fertilizer and chemical fertilizer+manure treatments. The metabolic ability of the bacterial community in the manure treatment was similar to the control. DGGE fingerprinting indicated similarity in the distribution of most 16S rDNA bands among all treatments,suggesting that microorganisms with those bands were stable and not infiuenced by fertilization. However,chemical fertilizer increased the diversity of soil bacterial community. Principal component analysis of Biolog and DGGE data revealed that the structure and function of the bacterial community were similar in the control and manure treatments,suggesting that the application of manure increased the soil microbial population,but had no effect on the bacterial community structure. Catabolic function was similar in the chemical fertilizer and chemical fertilizer+manure treatments,but the composition structure of the soil microbes differed between them. The use of chemical fertilizers could result in a decline in the catabolic activity of fast-growing or eutrophic bacteria.

Phylogenetic diversity of bacteria associated with the marine sponge Agelas robusta from South China Sea

It is well known that marine sponges harbor large numbers of bacteria,some of which have been proved to be sponge-specific.The diversity of bacteria in marine sponges distributed along the coast of South China Sea has been previously studied but that of bacteria in sponges inhabiting the open sea has been rarely investigated.In this report,the diversity of bacteria associated with the marine sponge Agelas robusta from a remote coral reef in the South China Sea was documented employing 16S rDNA library construction,amplified ribosomal DNA restriction analysis（ARDRA） and phylogenetic analysis.A total of 32 phylotypes were finally categorized in nine phyla including Cyanobacteria,Proteobacteria,Chloroflexi,Firmicutes,Actinobacteria,Acidobacteria,Planctomycetes,Bacteroidetes and Gemmatimonadetes.The dominant phylum was Proteobacteria whereas the dominant genus was Synechococcus in Cyanobacteria.Some spongespecific bacteria were also found in the bacteria population,but the proportion（5 OTUs/32 OTUs） was much lower than other sponges.This study reveals the phylogenetic diversity of bacteria in A.robusta and confirms the presence of some sponge-specific bacteria in the South China Sea.Understanding the diversity of sponge-associated bacteria in China assists to exploit the bacteria resources for biotechnology.

Phylogenetic diversity of planktonic bacteria in the Chukchi Borderland region in summer

Planktonic bacteria are abundant in the Chukchi Borderland region. However, little is known about their di- versity and the roles of various bacteria in the ocean. Seawater samples were collected from two stations K2S and K4S where sea ice was melting obviously. The analysis of water samples with fluorescence in situ hybridization （FISH） showed that DMSP-degrading bacteria accounted for 13% of the total bacteria at the station K2S. No aerobic anoxygenic phototrophic （AAP） bacteria were detected in both samples. The bacterial communities were characterized by two 16S rRNA gene clone libraries. Sequences fell into four major lineages of the domain Bacteria, including Proteobacteria （Alpha, Beta and Gamma subclasses）, Bac- teroidetes, Actinobacteria and Firmicutes. No significant difference was found between the two clone li- braries. SAR11 and Rhodobacteraceae clades of Alphaproteobacteria and Pseudoalteromonas of Gammapro- teobacteria constituted three dominant fractions in the clone libraries. A total of 191 heterotrophic bacterial strains were isolated and 76% showed extracellular proteolytic activity. Phylogenetic analysis reveals that the isolates fell into Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. The most common genus in both the bacterial isolates and protease-producing bacteria was Pseudoalteromonas. UniFrac data showed suggestive differences in bacterial communities between the Chukchi Borderland and the northern Bering Sea.

PCR-DGGE analysis of earthworm gut bacteria diversity in stress of <i>Escherichia coli</i>O157:H7

In order to test if the intestinal bacteria play an important role in antibacterial ability of earthworm, we chose Escherichia coli O157:H7, an anthropozoonosis pathogen, as a biological stressor and studied the change of intestinal bacteria community of earthworm by PCR-DGGE analysis. Results showed that the pathogen merely existed 1 - 3 days, then almost disappeared after through the earthworm’s gut. In this period, the diversity and abundance index of intestinal bacteria increased first, then decreased, and finally kept stably after 7 days. The result demonstrated that the intestinal bacteria of earthworm had ability of adjust community structure to eliminate the pathogen E. coli O157:H7, and the amount of bacteria Bacillus increased significantly, which might be the positive antagonism to E. coli O157:H7.

Morphological and phylogenetic diversity of magnetotactic bacteria and multicellular magnetotactic prokaryotes from a mangrove ecosystem in the Sanya River,South China

Magnetotactic bacteria(MTB)are morphologically and phylogenetically diverse prokaryotes commonly able to produce magnetic nanocrystals within intracellular membrane-bound organelles(i.e.,magnetosomes)and to swim along geomagnetic field lines.We studied the diversity of MTB in the samples collected from a mangrove area in the Sanya River,Hainan,South China,using microscopic and microbial phylogenetic methods.Results of microanalysis and observation in microscopy and energy dispersive X-ray spectroscopy(EDXS)reveal a highly morphological diversity of MTB including unicellular cocci,vibrios,rod-shaped bacteria,and three morphotypes of multicellular magnetotactic prokaryotes(MMPs).In addition,analysis of the 16S rRNA gene showed that these MTB were clustered into 16 operational taxonomic units affi liated to the Alpha-,Delta-,and Gamma-proteobacteria classes within the Proteobacteria phylum.Meanwhile,by using the coupled fluorescence and transmission electron microscopy analysis,rodshaped bacteria,vibrio,and cocci were phylogenetically and structurally identified at the single-cell level.This study demonstrated highly diverse MTB communities in the mangrove ecosystem and provide a new insight into the overall diversity of MTB.

Study on Endophytic Bacteria Diversity in the Root of Peperomia dindygulensis Miq. by Applying Clone Library Construction Method

[Objectives] To study the endophytic bacteria diversity in the root of Peperomia dindygulensis Miq. [Methods] The root of P.dindygulensis Miq. was taken as materials,culture-independent method was applied to build 16 S rDNA clone library for endophytic bacteria of P. dindygulensis Miq. [Results] In the 16 S rDNA clone library for endophytic bacteria of P. dindygulensis Miq.,95 clones separately belonged to 46 OTUs,Phylogenetic analysis indicated that these cloning sequences separately belonged to phylum Proteobacteria,phylum Bacteroidetes,phylum Actinobacteria,phylum Nitrospirae,and phylum Gemmatimonadetes. In these,phylum Proteobacteria accounted for 70. 53% of total number of clones,so it was the most dominant group in this library. [Conclusions]The endophytic bacteria diversity in the root of P.dindygulensis Miq. is rich and this study is expected to provide scientific basis for protection,development and use of resources of P. dindygulensis Miq.

Phylogenetic diversity of culturable bacteria in surface seawater from the Drake Passage,Antarctica

The Drake Passage is located between the Antarctic Peninsula and Tierra del Fuego in the south of South America.Surface seawater samples were collected at seven sites in the Drake Passage during the austral summer of 2012.The 16 S rRNA sequences were analyzed from 187 isolated bacterial strains.Three phyla,29 genera and 56 species were identified.The three phyla were Actinobacteria,Firmicutes and Proteobacteria;the Proteobacteria included a-Proteobacteria,P-Proteobacteria and y-Proteobacteria.y-Proteobacteria,Actinobacteria and Firmicutes were the dominant class or phyla in terms of quantity and species.Gram-positive bacteria(Actinobacteria and Firmicutes) accounted for 57.8% of all types identified.There were nine dominant genera,including Curtobacterium,Staphylococcus,and Halomonas,and 14 dominant species including Curtobacterium flaccumfaciens,Curtobacterium pusillum,and Staphylococcus sciuri.Of the strains identified,87.2% were catalase positive or weakly positive.

Characterization and diversity of magnetotactic bacteria from sediments of Caroline Seamount in the Western Pacific Ocean

Magnetotactic bacteria(MTB)are a group of microorganisms capable of orientating and swimming along magnetic fields because they contain intracellular biomineralized magnetosomes composed of magnetite(Fe 3 O 4)or/and greigite(Fe_(3)S_(4)).They are ubiquitous in freshwater,brackish,and marine habitats,and are cosmopolitan in distribution.However,knowledge of their occurrence and distribution in seamount ecosystems is limited.We investigated the diversity and distribution of MTB in the Caroline Seamount(CM4).The abundance of living MTB in 12 stations in depth varying from 90 to 1545 m was 1.1×10^(3)-43.7×10^(3) inds./dm 3.Despite diverse shapes of MTB observed,magnetotactic cocci were the dominant morphotype and could be categorized into two types:1)typical cocci that appeared to have peritrichous fl agella;and 2)those characterized by having a drop-shaped form and one bundle of fl agella located at the thin/narrow end of the cell.Transmission electron microscopy(TEM)analysis revealed that the magnetosomes formed by those magnetotactic cocci are magnetite(Fe 3 O 4)with octahedral crystal habit.A total of 41 operational taxonomic units(OTUs)of putative MTB(2702 reads)were acquired from nine stations,based on high-throughput sequencing.Of these,40 OTUs belonged to the Proteobacteria phylum and one belonged to the Nitrospirae phylum.We found apparent connectivity between the MTB populations on the Caroline and Kexue(Science in Chinese)seamounts,although the diversity of MTB on Caroline was much richer than on the Kexue Seamount.Our results imply that the unique topography of seamounts and other as-yet unclear environmental factors could lead to evolution of different fl agella arrangements in magnetotactic cocci,and the occurrence of octahedral magnetite magnetosomes.

Bacterial Community Diversity of Fermented Pepper in Brazzaville Revealed by Illumina Miseq of 16S rRNA Gene

Fermented foods play an important role in the daily life and diet of the populations in Congo. Among these fermented foods, there is Pilipili or fermented pepper which is consumed without prior cooking. The microorganisms present are eaten alive. Few studies have been carried out on these microorganisms which may have beneficial effects on health. This study aimed to investing taxonomic diversity of bacterial communities in 3 samples of fermented peppers produced in 3 distinct areas of Brazzaville. To do this investigation, Illumina Miseq sequencing of 16S rRNA gene was used. The results showed that the number of identified operational taxonomic units (OTUs) ranged from 156 to 392. All OTUs belong to the domain of Bacteria and could be categorized into 21 Phyla, 36 Classes, 58 Orders, 100 Families and 171 genera. Firmicutes and Proteobacteria were the main dominant phyla of the total phyla present with a relative abundance of 89.12% and 8.08%, respectly. At the class level, Bacili were dominant in EB1 (99.50%), EB3 (85.32%) and EB2 (42.29%) while Clostridia in EB2 (40.10%). Lactobacillus, Clostridium sensu stricto and Frutobacillus were the dominant genera in the sample EB1, EB2 and EB3, respectively. The hierarchical classification showed that the samples EB1 and EB2 form the same group and EB3 is unique. Principal component analysis showed that the younger EB3 and EB2 samples were more diverse than the older EB1 sample. This study is a first in Congo on the diversity of fermented pepper using Illumina Miseq. It has shown that this food is very diverse and can be a source for the isolation of bacteria with biotechnological potential.

Culturable bacterial diversity in hypolithic and peripheral soils in the west of the Hexi Corridor desert and its influencing factors

Microbes inhabiting the desert respond sensitively to environmental changes and may be an indicator for changes in the desert ecosystem.Hypolithic microbial communities in the desert play a vital role in ecosystem processes such as soil formation and organic matter accumulation.This study investigated and compared the culturable bacterial community structure and diversity in hypolithic and peripheral soils,and the interaction between bacteria and environmental factors.The bacteria were isolated using four different kinds of media and identified by 16S rRNA gene-sequence analysis.The numbers of culturable bacteria in the hypolithic and peripheral soils ranged from 3.0×104 to 3.6×105 CFU/g and from 6.5×104 to 5.3×105 CFU/g,respectively,indicating that the bacteria number in peripheral soil was higher than that in hypolithic soil.A total of 98 species belonging to 34 genera were identified,among which Arthrobacter,Bacillus,and Streptomyces were found dominantly and widely distributed.The community of culturable bacteria had obvious sample specificity,and the diversity in hypolithic soil was higher than that in peripheral soil.On the regional scale,the distribution of culturable bacteria and the environmental factors showed regular changes.On the local scale,the high heterogeneity of the hypolithic environment determined the specificity of the number and species of culturable bacteria.

Analyses on Community Composition and Diversity of Endophytic Bacteria in Different Tissues of Anoectochilus roxburghii

[Objective] This study aimed to investigate the diversity of community composition and diversity of endophytic bacteria in Anoectochilus roxburghii.[Method] By using Illumina MiSeq high-throughput sequencing technology, the 16S rDNA-V4 region of endophytic bacteria in ^4. roxburghii was sequenced. Qiime and Mothur software packages were used to sort and count the number of sequences and operational taxonomic units （OTUs） and analyze the species abundance and distribution, Alpha diversity and differences of species abundance among samples. [Result] The number of effective sequences/OTUs for each sample was 110485/247 （stem） and 98524/259 （leaf） , respectively. The rarefaction curve showed that adequate sampling was performed. The number of OTUs had almost reached a saturation point. Endophytic bacteria in A. roxburghii mainly belonged to the genera Acidovorax, Pseudomonas, Sphingomonas and Halomonas. [Conclusions] Illumi-na MiSeq high-throughput sequencing technology provides more accurate and scientific data resources for the study of endophytic bacteria in A. roxburghii.

Study of Bacterial Diversity of Mangroves Rhizosphere

Microbial diversity has been an important facet of scientific research, since microbes promise a plethora of biomolecules which are otherwise not found in nature. Microbes are subjected to high level of competition for survival in the environment, and hence develop mechanisms of defense. The biomolecules produced by these microbes as part of their defense or survival mechanism, are of importance for human and animal drugs and many other industrial and environmental applications. The marine counterparts of these terrestrial microbes have yet higher potential, since the marine environment has higher biotic and abiotic stresses, leading to new molecule discovery. In the current study, a bacterial diversity study of the culturable bacteria of the mangrove rhizosphere of Avicennia marina has been undertaken, to understand the flora diversity. Mangroves are unique ecosystems which are under a combination of marine and terrestrial influence. Mangroves are seaward, inland and also found in creek areas. This diversity in their habitat, leads them to produce variable root exudates, which support the growth of different types of organisms. This study has revealed that certain species are dominant in these ecosystems irrespective of the biotic and abiotic stresses, whereas certain species appear only at neutral pH. The study will help select organisms for further biomolecule discovery programs, based on their environment of isolation and other growth parameters.